I will focus on the early events in the working cycle of a biological nanomachine, chaperonin GroEL, in this study. I will perform computer simulations of a protein binding to GroEL, concentrating on protein recruitment and recognition mechanisms and conformational changes in the substrate protein and GroEL. I will investigate folding and unfolding upon binding and the effect of protein load on the GroEL functional cycle. I will use both coarse-grained and all-atom simulations, taking advantage of the simulation lengths and simplifying power of the first approach and detailed view of the second approach. This research will clarify the inner workings of chaperonins and also add to our knowledge of protein-protein interactions in general. Because protein misfolding and aggregation are held responsible for many diseases such as Alzheimer's and Parkinson's diseases, learning how chaperonins, our natural defense mechanisms, function, will, in the future, help us fight them. Better understanding of chaperonins is also needed to cure diseases that have been directly linked to human chaperonins'malfunctioning such as hereditary spastic paraplegia or McKusick-Kaufman Syndrome. I envision that the knowledge and techniques acquired from this research will later be employed in studying other biological nanomachines that are essential to the normal functioning of our bodies and also other protein-protein interactions that direct countless biological functions.